TOKYO—Japan’s trade deficit edged up in September despite a rebound in exports helped by a weaker yen and a surge in output among suppliers of Apple Inc.’s new smartphones.

The latest figures, released Wednesday by Japan’s finance ministry, again demonstrate the mixed impact of a weaker currency on the nation’s trade balance.

While a weaker yen helps inflate the value of Japan’s exports in the short run and could help boost volume in the longer run, it also increases the bill for imports. In September, the Japanese currency fell to a six-year low close to ¥110 to the dollar.

The trade data showed that exports grew 6.9% in September from a year earlier, while imports rose 6.2%. Exports of parts for the new iPhones helped boost the export figure, while a large increase in natural gas imports added a volatile element to the import figure, ministry data showed.

The overall impact on the nation’s trade balance was to push up the deficit by 1.6% to ¥958.3 billion ($8.96 billion) from a year earlier, the first increase in three months. That compared with a median forecast for a ¥768 billion deficit in a survey of economists by The Wall Street Journal and the Nikkei.

The record 27th straight monthly trade shortfall comes amid continued offshoring by Japanese multinationals—a trend economists say reduces the beneficial impact of a weaker yen on boosting export volumes. The September data showed that auto exports to the U.S. in September fell for the sixth month, despite strong sales among Japan’s car makers in the North American market.

The lengthy run of deficits also reflects Japan’s energy woes. The nation’s nuclear power plants have been kept offline as a result of the 2011 Fukushima nuclear accident, leaving the country reliant on fossil fuel for 90% of electricity generation, up from around 60% before the accident.

Japan’s trade data followed upbeat trade figures from China and South Korea released earlier in the month. For the month of September, China reported a 15% jump in exports and a 7% rise in imports. South Korea said its exports and imports grew 7% and 8%, respectively. Both countries import Japanese electronics components and produce smartphones and other electronics devices for exports world-wide.